A5069094618- Astrophysics and Cosmic Phenomena
- Ionosphere and magnetosphere dynamics
- Geophysics and Gravity Measurements
- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Bioinformatics and Genomic Networks
- Microbial Metabolic Engineering and Bioproduction
- Gene expression and cancer classification
- Gut microbiota and health
- Scientific Computing and Data Management
- Microfluidic and Bio-sensing Technologies
- Genetic diversity and population structure
- Microbial Fuel Cells and Bioremediation
- Atmospheric and Environmental Gas Dynamics
- Innovative Microfluidic and Catalytic Techniques Innovation
- Wastewater Treatment and Nitrogen Removal
- Microfluidic and Capillary Electrophoresis Applications
- Algorithms and Data Compression
- Machine Learning in Bioinformatics
- Metabolomics and Mass Spectrometry Studies
- Complex Network Analysis Techniques
- Methane Hydrates and Related Phenomena
- Experimental Learning in Engineering
- Molecular Communication and Nanonetworks
- Energy Efficient Wireless Sensor Networks
University of British Columbia
2012-2023
KPMG (United States)
2016
Genome British Columbia
2014-2015
Planktonic bacteria dominate surface ocean biomass and influence global biogeochemical processes, but remain poorly characterized owing to difficulties in cultivation. Using large-scale single cell genomics, we obtained insight into the genome content biogeography of many bacterial lineages inhabiting ocean. We found that, compared with existing cultures, natural bacterioplankton have smaller genomes, fewer gene duplications, are depleted guanine cytosine, noncoding nucleotides, genes...
We present a programmable droplet-based microfluidic device that combines the reconfigurable flow-routing capabilities of integrated microvalve technology with sample compartmentalization and dispersion-free transport is inherent to droplets. The allows for execution user-defined multistep reaction protocols in 95 individually addressable nanoliter-volume storage chambers by consecutively merging sequences picoliter-volume droplets containing reagents or cells. This functionality enabled...
Oil in subsurface reservoirs is biodegraded by resident microbial communities. Water-mediated, anaerobic conversion of hydrocarbons to methane and CO2, catalyzed syntrophic bacteria methanogenic archaea, thought be one the dominant processes. We compared 160 community compositions ten hydrocarbon resource environments (HREs) sequenced twelve metagenomes characterize their metabolic potential. Although communities were common, cores from oil sands coal beds had unexpectedly high proportions...
Abstract Background A central challenge to understanding the ecological and biogeochemical roles of microorganisms in natural human engineered ecosystems is reconstruction metabolic interaction networks from environmental sequence information. The dominant paradigm assign functional annotations using BLAST. Functional are then projected onto symbolic representations metabolism form KEGG pathways or SEED subsystems. Results Here we present MetaPathways, an open source pipeline for pathway...
Marine Group A (MGA) is a deeply branching and uncultivated phylum of bacteria. Although their functional roles remain elusive, MGA subgroups are particularly abundant diverse in oxygen minimum zones permanent or seasonally stratified anoxic basins, suggesting metabolic adaptation to oxygen-deficiency. Here, we expand previous survey diversity O2-deficient waters the Northeast subarctic Pacific Ocean (NESAP) include Saanich Inlet (SI), an fjord with seasonal O2 gradients periodic sulfide...
Summary Enhanced biological phosphorus removal ( EBPR ) relies on diverse but specialized microbial communities to mediate the cycling and ultimate of from municipal wastewaters. However, little is known about activity dynamics in relation process fluctuations ecosystems. Here, we monitored temporal changes community structure potential across each bioreactor zone a pilot‐scale treatment plant by examining ratio small subunit ribosomal RNA SSU r gene (r DNA over 120 day study period....
A convergence of high-throughput sequencing and computational power is transforming biology into information science. Despite these technological advances, converting bits bytes sequence meaningful insights remains a challenging enterprise. Biological systems operate on multiple hierarchical levels from genomes to biomes. Holistic understanding biological requires agile software tools that permit comparative analyses across (DNA, RNA, protein, metabolites) identify emergent properties,...
Abstract Summary: Next-generation sequencing is producing vast amounts of sequence information from natural and engineered ecosystems. Although this data deluge has an enormous potential to transform our lives, knowledge creation translation need software applications that scale with increasing processing analysis requirements. Here, we present improvements MetaPathways, annotation pipeline for environmental expedites transformation. We specifically address pathway prediction hazards through...
Pairwise comparison of time series data for both local and time-lagged relationships is a computationally challenging problem relevant to many fields inquiry. The Local Similarity Analysis (LSA) statistic identifies the existence lagged relationships, but determining significance through p-value has been algorithmically cumbersome due an intensive permutation test, shuffling rows columns repeatedly calculating statistic. Furthermore, this calculated with assumption normality -- statistical...
Motivation: A perennial problem in the analysis of environmental sequence information is assignment reads or assembled sequences, e.g. contigs scaffolds, to discrete taxonomic bins. In absence reference genomes for most microorganisms, use intrinsic nucleotide patterns and phylogenetic anchors can improve assembly-dependent binning needed more accurate functional annotation communities assist identifying mobile genetic elements lateral gene transfer events. Results: Here, we present a...
A fundamental step in the analysis of environmental sequence information is prediction potential genes or open reading frames (ORFs) encoding metabolic individual cells and entire microbial communities. FragGeneScan, a software designed to predict intact incomplete ORFs on short sequencing reads combines codon usage bias, error models start/stop patterns hidden Markov model find most likely path states from given input sequence, provides promising route for gene recovery datasets with...
The development of high-throughput sequencing technologies over the past decade has generated a tidal wave environmental sequence information from variety natural and human engineered ecosystems. resulting flood into public databases archived projects exponentially expanded computational resource requirements rendering most local homology-based search methods inefficient. We recently introduced MetaPathways v1.0, modular annotation analysis pipeline for constructing Pathway/Genome Databases...
Advances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body, with implications for therapeutic interventions. Several large-scale datasets derived from hundreds of microbiome samples sourced multiple studies now publicly available. However, idiosyncratic data processing methods between introduce systematic differences that confound comparative analyses. To overcome these challenges, developed GutCyc, a compendium environmental pathway...
FAST is a multi-threaded, I/O optimized Seed-and-Extend alignment program. extensible to nucleotide sequences making it comparable both BLASTn and BLASTp, also features several new usage flags reporting only HSPs meeting user defined e-value cut-offs. FASTs threaded database construction allows fast, low memory e.g., RefSeq (9.4GB) can be indexed in under 5 minutes using 20 threads. The gives users the ability create custom databases on demand which useful for tasks requiring self-alignment,...
Accurate description of the microbial communities driving matter and energy transformations in complex ecosystems such as soils cannot yet be effectively accomplished using assembly-based approaches despite rise next generation sequencing technologies. Here we present SOFA, an open source pipeline enabling comparative functional annotation unassembled short-read data. The attempts to merge mate pairs fastq files, predicts reading frames (ORFs) on merged unmerged reads small 70 bps, completes...
Abstract Advances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body, with implications for therapeutic interventions. Several large-scale datasets derived from hundreds of microbiome samples sourced multiple studies now publicly available. However, idiosyncratic data processing methods between introduce systematic differences that confound comparative analyses. To overcome these challenges, developed G UT C YC , a compendium...